PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1YL7
Asym. Unit
Info
Asym.Unit (317 KB)
Biol.Unit 1 (157 KB)
Biol.Unit 2 (155 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DIHYDRODIPICOLINATE REDUCTASE (RV2773C) IN COMPLEX WITH NADH (CRYSTAL FORM C)
Authors
:
R. Janowski, G. Kefala, M. S. Weiss, Tb Structural Genomics Consort (Tbsgc)
Date
:
19 Jan 05 (Deposition) - 17 Jan 06 (Release) - 30 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.34
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Lysine Biosynthesis, Dihydrodipicolinate, Reductase, Nadh, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Janowski, G. Kefala, M. S. Weiss
The Structure Of Dihydrodipicolinate Reductase (Dapb) From Mycobacterium Tuberculosis In Three Crystal Forms.
Acta Crystallogr. , Sect. D V. 66 61 2010
[
close entry info
]
Hetero Components
(2, 14)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
2a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
2b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
2c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
2d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
2e: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIe)
2f: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIf)
2g: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIg)
2h: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
6
Ligand/Ion
MAGNESIUM ION
2
NAI
8
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL D:20 , ALA D:21 , ALA D:23 , LEU D:26 , HOH D:505 , HOH D:585
BINDING SITE FOR RESIDUE MG D 401
02
AC2
SOFTWARE
VAL G:20 , ALA G:21 , ALA G:23 , LEU G:26 , HOH G:511
BINDING SITE FOR RESIDUE MG G 402
03
AC3
SOFTWARE
VAL E:20 , ALA E:21 , ALA E:23 , LEU E:26
BINDING SITE FOR RESIDUE MG E 403
04
AC4
SOFTWARE
VAL B:20 , ALA B:21 , ALA B:23 , LEU B:26 , HOH B:555
BINDING SITE FOR RESIDUE MG B 404
05
AC5
SOFTWARE
VAL A:20 , ALA A:21 , ALA A:23 , LEU A:26
BINDING SITE FOR RESIDUE MG A 405
06
AC6
SOFTWARE
VAL F:20 , ALA F:21 , ALA F:23 , LEU F:26
BINDING SITE FOR RESIDUE MG F 406
07
AC7
SOFTWARE
GLY A:7 , LYS A:9 , GLY A:10 , LYS A:11 , VAL A:12 , LEU A:32 , ASP A:33 , ALA A:34 , PHE A:52 , THR A:53 , VAL A:57 , GLY A:75 , THR A:76 , THR A:77 , ALA A:102 , PRO A:103 , ASN A:104 , PHE A:105 , PHE A:217 , HOH A:503 , HOH A:512
BINDING SITE FOR RESIDUE NAI A 501
08
AC8
SOFTWARE
GLY B:7 , LYS B:9 , GLY B:10 , LYS B:11 , VAL B:12 , LEU B:32 , ASP B:33 , ALA B:34 , PHE B:52 , THR B:53 , VAL B:57 , GLY B:75 , THR B:76 , THR B:77 , ALA B:102 , PRO B:103 , ASN B:104 , PHE B:105 , PHE B:217 , HOH B:516
BINDING SITE FOR RESIDUE NAI B 502
09
AC9
SOFTWARE
GLY C:7 , LYS C:9 , GLY C:10 , LYS C:11 , VAL C:12 , ASP C:33 , ALA C:34 , PHE C:52 , THR C:53 , VAL C:57 , GLY C:75 , THR C:77 , ALA C:102 , PRO C:103 , ASN C:104 , PHE C:105 , PHE C:217 , HOH C:529
BINDING SITE FOR RESIDUE NAI C 503
10
BC1
SOFTWARE
SER C:166 , THR C:167 , HOH C:505 , GLY D:7 , LYS D:9 , GLY D:10 , LYS D:11 , VAL D:12 , ASP D:33 , ALA D:34 , PHE D:52 , THR D:53 , VAL D:57 , GLY D:75 , THR D:77 , ALA D:102 , PRO D:103 , ASN D:104 , PHE D:105 , PHE D:217 , HOH D:510 , HOH D:511 , HOH D:524 , HOH D:527 , HOH D:546 , HOH D:580
BINDING SITE FOR RESIDUE NAI D 504
11
BC2
SOFTWARE
GLY E:7 , LYS E:9 , GLY E:10 , LYS E:11 , VAL E:12 , ASP E:33 , ALA E:34 , PHE E:52 , THR E:53 , VAL E:57 , GLY E:75 , THR E:76 , THR E:77 , ALA E:102 , PRO E:103 , ASN E:104 , PHE E:105 , PHE E:217 , HOH E:507
BINDING SITE FOR RESIDUE NAI E 505
12
BC3
SOFTWARE
LEU F:6 , GLY F:7 , GLY F:10 , LYS F:11 , VAL F:12 , ASP F:33 , ALA F:34 , PHE F:52 , THR F:53 , VAL F:57 , GLY F:75 , THR F:76 , THR F:77 , ALA F:102 , PRO F:103 , ASN F:104 , PHE F:105 , HOH F:513
BINDING SITE FOR RESIDUE NAI F 506
13
BC4
SOFTWARE
LEU G:6 , GLY G:7 , LYS G:9 , GLY G:10 , LYS G:11 , VAL G:12 , LEU G:32 , ASP G:33 , ALA G:34 , PHE G:52 , THR G:53 , GLY G:75 , THR G:76 , THR G:77 , ALA G:102 , PRO G:103 , ASN G:104 , PHE G:105 , PHE G:217 , HOH G:508 , HOH G:524 , HOH G:563
BINDING SITE FOR RESIDUE NAI G 507
14
BC5
SOFTWARE
GLY H:7 , LYS H:9 , GLY H:10 , LYS H:11 , VAL H:12 , ASP H:33 , ALA H:34 , PHE H:52 , THR H:53 , VAL H:57 , GLY H:75 , THR H:77 , ALA H:102 , PRO H:103 , ASN H:104 , PHE H:105 , PHE H:217 , HOH H:515
BINDING SITE FOR RESIDUE NAI H 508
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: DAPB (A:127-144,B:127-144,C:127-144,D:12...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DAPB
PS01298
Dihydrodipicolinate reductase signature.
DAPB_MYCTO
127-144
8
A:127-144
B:127-144
C:127-144
D:127-144
E:127-144
F:127-144
G:127-144
H:127-144
DAPB_MYCTU
127-144
8
A:127-144
B:127-144
C:127-144
D:127-144
E:127-144
F:127-144
G:127-144
H:127-144
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1yl7a2 (A:106-214)
1b: SCOP_d1yl7g2 (G:106-214)
1c: SCOP_d1yl7h2 (H:106-214)
1d: SCOP_d1yl7b2 (B:106-214)
1e: SCOP_d1yl7c2 (C:106-214)
1f: SCOP_d1yl7d2 (D:106-214)
1g: SCOP_d1yl7e2 (E:106-214)
1h: SCOP_d1yl7f2 (F:106-214)
2a: SCOP_d1yl7a1 (A:2-105,A:215-245)
2b: SCOP_d1yl7g1 (G:2-105,G:215-245)
2c: SCOP_d1yl7h1 (H:2-105,H:215-245)
2d: SCOP_d1yl7b1 (B:2-105,B:215-245)
2e: SCOP_d1yl7c1 (C:2-105,C:215-245)
2f: SCOP_d1yl7d1 (D:2-105,D:215-245)
2g: SCOP_d1yl7e1 (E:2-105,E:215-245)
2h: SCOP_d1yl7f1 (F:2-105,F:215-245)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
Dihydrodipicolinate reductase-like
(45)
Protein domain
:
Dihydrodipicolinate reductase
(11)
Mycobacterium tuberculosis [TaxId: 1773]
(5)
1a
d1yl7a2
A:106-214
1b
d1yl7g2
G:106-214
1c
d1yl7h2
H:106-214
1d
d1yl7b2
B:106-214
1e
d1yl7c2
C:106-214
1f
d1yl7d2
D:106-214
1g
d1yl7e2
E:106-214
1h
d1yl7f2
F:106-214
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Dihydrodipicolinate reductase
(11)
Mycobacterium tuberculosis [TaxId: 1773]
(5)
2a
d1yl7a1
A:2-105,A:215-245
2b
d1yl7g1
G:2-105,G:215-245
2c
d1yl7h1
H:2-105,H:215-245
2d
d1yl7b1
B:2-105,B:215-245
2e
d1yl7c1
C:2-105,C:215-245
2f
d1yl7d1
D:2-105,D:215-245
2g
d1yl7e1
E:2-105,E:215-245
2h
d1yl7f1
F:2-105,F:215-245
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1yl7A02 (A:106-212)
1b: CATH_1yl7E02 (E:106-212)
1c: CATH_1yl7F02 (F:106-212)
1d: CATH_1yl7G02 (G:106-212)
1e: CATH_1yl7H02 (H:106-212)
1f: CATH_1yl7B02 (B:106-212)
1g: CATH_1yl7C02 (C:106-212)
1h: CATH_1yl7D02 (D:106-212)
2a: CATH_1yl7A01 (A:1-105,A:213-245)
2b: CATH_1yl7B01 (B:1-105,B:213-245)
2c: CATH_1yl7C01 (C:1-105,C:213-245)
2d: CATH_1yl7D01 (D:1-105,D:213-245)
2e: CATH_1yl7E01 (E:1-105,E:213-245)
2f: CATH_1yl7F01 (F:1-105,F:213-245)
2g: CATH_1yl7G01 (G:1-105,G:213-245)
2h: CATH_1yl7H01 (H:1-105,H:213-245)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(5)
1a
1yl7A02
A:106-212
1b
1yl7E02
E:106-212
1c
1yl7F02
F:106-212
1d
1yl7G02
G:106-212
1e
1yl7H02
H:106-212
1f
1yl7B02
B:106-212
1g
1yl7C02
C:106-212
1h
1yl7D02
D:106-212
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(22)
2a
1yl7A01
A:1-105,A:213-245
2b
1yl7B01
B:1-105,B:213-245
2c
1yl7C01
C:1-105,C:213-245
2d
1yl7D01
D:1-105,D:213-245
2e
1yl7E01
E:1-105,E:213-245
2f
1yl7F01
F:1-105,F:213-245
2g
1yl7G01
G:1-105,G:213-245
2h
1yl7H01
H:1-105,H:213-245
[
close CATH info
]
Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_DapB_N_1yl7H01 (H:2-105)
1b: PFAM_DapB_N_1yl7H02 (H:2-105)
1c: PFAM_DapB_N_1yl7H03 (H:2-105)
1d: PFAM_DapB_N_1yl7H04 (H:2-105)
1e: PFAM_DapB_N_1yl7H05 (H:2-105)
1f: PFAM_DapB_N_1yl7H06 (H:2-105)
1g: PFAM_DapB_N_1yl7H07 (H:2-105)
1h: PFAM_DapB_N_1yl7H08 (H:2-105)
2a: PFAM_DapB_C_1yl7H09 (H:108-242)
2b: PFAM_DapB_C_1yl7H10 (H:108-242)
2c: PFAM_DapB_C_1yl7H11 (H:108-242)
2d: PFAM_DapB_C_1yl7H12 (H:108-242)
2e: PFAM_DapB_C_1yl7H13 (H:108-242)
2f: PFAM_DapB_C_1yl7H14 (H:108-242)
2g: PFAM_DapB_C_1yl7H15 (H:108-242)
2h: PFAM_DapB_C_1yl7H16 (H:108-242)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
DapB_N
(5)
Mycobacterium tuberculosis
(4)
1a
DapB_N-1yl7H01
H:2-105
1b
DapB_N-1yl7H02
H:2-105
1c
DapB_N-1yl7H03
H:2-105
1d
DapB_N-1yl7H04
H:2-105
1e
DapB_N-1yl7H05
H:2-105
1f
DapB_N-1yl7H06
H:2-105
1g
DapB_N-1yl7H07
H:2-105
1h
DapB_N-1yl7H08
H:2-105
Clan
:
no clan defined [family: DapB_C]
(5)
Family
:
DapB_C
(5)
Mycobacterium tuberculosis
(4)
2a
DapB_C-1yl7H09
H:108-242
2b
DapB_C-1yl7H10
H:108-242
2c
DapB_C-1yl7H11
H:108-242
2d
DapB_C-1yl7H12
H:108-242
2e
DapB_C-1yl7H13
H:108-242
2f
DapB_C-1yl7H14
H:108-242
2g
DapB_C-1yl7H15
H:108-242
2h
DapB_C-1yl7H16
H:108-242
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (317 KB)
Header - Asym.Unit
Biol.Unit 1 (157 KB)
Header - Biol.Unit 1
Biol.Unit 2 (155 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1YL7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help